Hi Sam.
Can you produce another bug report.
Please don't attach files to these mails as it will strain the
mailinglists.
Cheers
Troels
Den lørdag den 10. september 2016 skrev Mahdi, Sam <
sam.mahdi....@my.csun.edu>:
> Hi Troels,
>
> Additional question that I had, if you could also look into this as well
> on Tuesday please. I have decided to try to write a script to automate this
> whole process (since I won't be using the gui to do model free), and I've
> come across a problem. I can successfully open up relax using openmpi, and
> can load the pdb file, and assign all the spins and isotopes; however, it
> appears it will only load one data file (the very first one I'll have
> inputed in the script). I don't know if there is a problem with how I wrote
> my script. Not only will it not load the rest of my data sets, it won't
> actually run dAuvergne's protocol either, it'll just load the data set and
> exit out of the program. Attached is the script I wrote for relax.
>
> This is the output once relax has loaded
>
> script = 'model_free_sample_script.py'
> ------------------------------------------------------------
> ----------------------------------------
> from time import asctime, localtime
> from auto_analyses.dauvergne_protocol import dAuvergne_protocol
> DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoid','final']
> MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']
> LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','
> tm7','tm7','tm8','tm9']
> GRID_INC=11
> MIN_ALGOR='newton'
> MC_NUM=500
> CONV_LOOP=True
> pipe_bundle="mf(%s)"%asctime(localtime())
> name="origin-"+pipe_bundle
> pipe.create(name,'mf',bundle=pipe_bundle)
> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')
> structure.load_spins('@N',ave_pos=True)
> structure.load_spins('@NE1',ave_pos=True)
> structure.load_spins('@H',ave_pos=True)
> structure.load_spins('@HE1',ave_pos=True)
> spin.isotope('15N',spin_id='@N*')
> spin.isotope('1H',spin_id='@H*')
> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
> file='R2_Agnes',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
> file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6,
> file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6,
> file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6,
> file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3)
> interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True)
> interatom.define(spin_id1='@NE1',spin_id2='@HE1', direct_bond=True)
> interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.02*1e-10)
> interatom.unit_vectors()
> value.set(-172*1e-6,'csa',spin_id='@N*')
> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,
> diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_
> models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_
> ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
>
> So it indicates that my script has loaded. However, after it loads the
> spins from the pdb file, this is what happens after my first data set has
> been loaded:
>
> relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', frq=599642000.0,
> file='R1_Agnes', dir=None, spin_id_col=None, mol_name_col=None,
> res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=None,
> data_col=2, error_col=3, sep=None, spin_id=None)
> Opening the file 'R1_Agnes' for reading.
> RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
> invalid, the residue number data 'Residue' is invalid.
> RelaxWarning: The sequence data in the line ['1'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['2'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['3'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['4'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['5'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['6'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['7'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['8'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['9'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['10'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['11'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['16'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['17'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['18'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['21'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['22'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['23'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['26'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['27'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['28'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['31'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['40'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['46'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['58'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['61'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['62'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['63'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['73'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['76'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['79'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['81'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['82'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['85'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['94'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['97'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['99'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['106'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['115'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['121'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['126'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['127'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['134'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['135'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['136'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['137'] is invalid, the data
> is missing.
> RelaxWarning: The sequence data in the line ['139'] is invalid, the data
> is missing.
>
> RelaxError: The spin ID '#hRGS7:12' corresponds to multiple spins,
> including '#hRGS7:12@N' and '#hRGS7:12@H'.
> crowlab: [~/relax-4.0.2]>
>
> As you can see, I have all 6 data sets set to load, but only the very
> first one appears to do so, and after it loads, it just exits out of relax.
> Again, I don't know if this is a problem with how I wrote the script. The
> Relax_script1 is the one that I load up to run the whole thing. The model
> free script.py is just the script it reads once relax has opened up.
> Again, I can see all the spins are properly loaded, and the isotopes are
> set. It just everything after the first data set that doesn't load. Thanks
> again in advance.
>
> Sincerely,
> Sam
>
> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu
> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>> wrote:
>
>> Hi Troels,
>>
>> Thank you so much. If there is any extra info you need please let me
>> know.
>>
>> Sincerely,
>> Sam
>>
>> On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com
>> <javascript:_e(%7B%7D,'cvml','tlin...@nmr-relax.com');>> wrote:
>>
>>> Hi Sam.
>>>
>>> I will have some time on Tuesday, and then I will look at it.
>>>
>>> Best
>>> Troels
>>>
>>>
>>> Den onsdag den 7. september 2016 skrev Mahdi, Sam <
>>> sam.mahdi....@my.csun.edu
>>> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>>:
>>>
>>>> Hello Troels,
>>>>
>>>> I uploaded all the files, and even added in the entire output that i
>>>> recieved using model free in script mode. I didn't know if all the files
>>>> uploaded need to have that link, so only the initial files that were
>>>> uploaded it, have it.
>>>> Thank you in advance for your help!
>>>> Sincerely,
>>>> Sam
>>>>
>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet <
>>>> tlin...@nmr-relax.com> wrote:
>>>>
>>>>> Hi Sam.
>>>>>
>>>>> You should be able to upload more files after the initial upload.
>>>>> In the comment thread, please also make a link to this discussion.
>>>>>
>>>>> https://mail.gna.org/public/relax-users/2016-09/threads.html#00001
>>>>>
>>>>> Best
>>>>> Troels
>>>>>
>>>>>
>>>>>
>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>
>>>>>> Thank you for your reply. When I come to upload my data though, I see
>>>>>> there are only 4 available slots I can upload my data. I have a total of
>>>>>> 6
>>>>>> data files however, that need to be uploaded (3 of each frequency). I
>>>>>> also
>>>>>> need to upload the relax -i of 2 different computers, and the script file
>>>>>> I've been using for a total of 9 files that need to be uploaded. Is
>>>>>> there a
>>>>>> way to increase the amount I can upload, or can I upload more after the
>>>>>> initial submission?
>>>>>>
>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>
>>>>>>> Hi Sam.
>>>>>>>
>>>>>>> To solve this problem, it would be easier to have access to some of
>>>>>>> your data.
>>>>>>> Can you upload to: https://gna.org/bugs/?group=relax
>>>>>>>
>>>>>>> Take each of your data files, and delete all data, except 2 spins.
>>>>>>> Also provide your script file, or a description of which button you
>>>>>>> press in the GUI.
>>>>>>>
>>>>>>> Please also provide information about your system with:
>>>>>>> relax -i
>>>>>>>
>>>>>>> Then I will make a tutorial for you. To be added here:
>>>>>>> http://wiki.nmr-relax.com/Category:Tutorials
>>>>>>>
>>>>>>> If there is a problem in relax, I will write a systemtest which will
>>>>>>> solve the problem.
>>>>>>> And the problem will never return.
>>>>>>>
>>>>>>> If this a user error, the tutorial should help to prevent this, and
>>>>>>> would be the first step before
>>>>>>> adding/modifying the manual.
>>>>>>>
>>>>>>> Regarding using mpirun.
>>>>>>> Have a look at this page. Maybe it helps.
>>>>>>> http://wiki.nmr-relax.com/OpenMPI
>>>>>>>
>>>>>>>
>>>>>>> Cheers.
>>>>>>>
>>>>>>>
>>>>>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>
>>>>>>>> Hello everyone,
>>>>>>>>
>>>>>>>> So I was able to set up and run the dauvergne_protocol successfully
>>>>>>>> by
>>>>>>>> using the script in the wiki. The problem I have come across now is
>>>>>>>> the
>>>>>>>> program doesn't seem to read my data. Using the gui interface I was
>>>>>>>> able to
>>>>>>>> successfully load my data and run it. When I upload my data using
>>>>>>>> the
>>>>>>>> script command:
>>>>>>>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
>>>>>>>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>>>>>>>>
>>>>>>>> The output file simply gives errors for amino acids I don't have
>>>>>>>> data for:
>>>>>>>> RelaxWarning: The sequence data in the line ['1'] is invalid, the
>>>>>>>> data is
>>>>>>>> missing.
>>>>>>>>
>>>>>>>> This is fine as relax just ignores these values and continues its
>>>>>>>> calculations. I only receive this warning for values I don't have
>>>>>>>> data for.
>>>>>>>> This is the same thing I got when using the gui interface (the gui
>>>>>>>> however
>>>>>>>> showed my values that I have data for and the residue it
>>>>>>>> corresponds to,
>>>>>>>> using the script I don't receive such an output, I don't know
>>>>>>>> whether this
>>>>>>>> is normal or not). However, since I don't get this warning for
>>>>>>>> every amino
>>>>>>>> acid, I assume this means it has read the values for the other
>>>>>>>> amino acids.
>>>>>>>> All of my data is the same, relax warnings only pop up for amino
>>>>>>>> acids that
>>>>>>>> I don't have data for. The problem is, when I enter the dAuvergne
>>>>>>>> protocol,
>>>>>>>> I get the protocol working, it starts running local_tm however it
>>>>>>>> appears
>>>>>>>> none of my data has been uploaded:
>>>>>>>> RelaxWarning: The spin '#hRGS7:2@N' has been deselected because of
>>>>>>>> missing
>>>>>>>> relaxation data
>>>>>>>> RelaxWarning: The spin '#hRGS7:3@N' has been deselected because of
>>>>>>>> missing
>>>>>>>> relaxation data
>>>>>>>>
>>>>>>>> And I get that warning for every single amino acid. From the
>>>>>>>> output, it
>>>>>>>> appears to have read the file since it knows exactly which amino
>>>>>>>> acids I
>>>>>>>> don't have data for, but I don't know why when it comes to running
>>>>>>>> the
>>>>>>>> protocol, it tells me I havn't inputed any data. I have typed
>>>>>>>> everything
>>>>>>>> directly according to the script from the wiki. From running the
>>>>>>>> protoco,
>>>>>>>> it appears everything has properly been uploaded, structure data,
>>>>>>>> magnetic
>>>>>>>> dipole interactions, csa, the data pipe, the analysis variables,
>>>>>>>> the python
>>>>>>>> module imports, and setting up the spins from the pdb file. It
>>>>>>>> appears the
>>>>>>>> only error is from loading the actual relaxation data.
>>>>>>>>
>>>>>>>> On a completely unrelated side note, I have been attempting to run
>>>>>>>> relax on
>>>>>>>> multiple processors. I have tried 2 different computers, both
>>>>>>>> fedora linux.
>>>>>>>> I have mpi4py and openmpi downloaded on both. On one, I can get
>>>>>>>> relax on
>>>>>>>> multiple cores working (havn't been able to successfully run it due
>>>>>>>> to
>>>>>>>> being unable to upload any data properly). On the other however, I
>>>>>>>> type in
>>>>>>>> the mpirun -np --multi='mpi4py' script, but I get no output. I can
>>>>>>>> see that
>>>>>>>> it's running in the background (top command), but nothing pops up,
>>>>>>>> no text
>>>>>>>> command, nothing. I typed the same mpirun with the --gui, but that
>>>>>>>> opened
>>>>>>>> up nothing. On a uni-processor (typing in the exact same command
>>>>>>>> without
>>>>>>>> indicating how many cores i.e. no -np --multi='mpi4py') it works
>>>>>>>> just fine,
>>>>>>>> so I don't think its my openmpi that's an issue. I don't know
>>>>>>>> whether this
>>>>>>>> is an issue with my mpi4py or a personal computer issue (since on
>>>>>>>> the other
>>>>>>>> computer relax runs just fine on multiple cores).
>>>>>>>>
>>>>>>>> Sincerely,
>>>>>>>> Sam
>>>>>>>>
>>>>>>>> P.S. when I do enter the top command to see what's running. My
>>>>>>>> master shows
>>>>>>>> mpirun, and the 3 slaves display python when I put -np 4, so I know
>>>>>>>> something is running in the background. I have 8 cores.
>>>>>>>>
>>>>>>>> On Wed, Aug 31, 2016 at 6:49 PM, Mahdi, Sam <
>>>>>>>> sam.mahdi....@my.csun.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> > Hello everyone,
>>>>>>>> >
>>>>>>>> > I am attempting to run relax on a multi-processor mode. I have
>>>>>>>> been able
>>>>>>>> > to successfully set-up relax to operate in a multi-processor mode
>>>>>>>> by using
>>>>>>>> > the mpirun -np #ofprocessors /location/of/relax --multi='mpi4py'
>>>>>>>> >
>>>>>>>> > The problem I encounter is when using the --tee log
>>>>>>>> dauvergne_protocol.py
>>>>>>>> > command. I receive this error
>>>>>>>> > RelaxError: the script file 'dauvergne_protocol.py' does not exist
>>>>>>>> >
>>>>>>>> > I located the script file and tried to direct to it's path
>>>>>>>> > mpirun /usr/local/Relax/relax-2.2.5/relax --multi='mpi4py' --tee
>>>>>>>> log
>>>>>>>> > /usr/local/Relax/relax-2.2.5/auto-analyses/dauvergne_protocol.py
>>>>>>>> >
>>>>>>>> > But i received this error
>>>>>>>> > RelaxError: the script file '/usr/local/Relax/relax-2.2.5/
>>>>>>>> > auto-analyses/dauvergne_protocol.py' does not exist.
>>>>>>>> >
>>>>>>>> > Even though I have the script, it doesn't seem to be able to
>>>>>>>> locate it.
>>>>>>>> >
>>>>>>>> > On a side note, in the manual, one dash doesn't actually run the
>>>>>>>> command.
>>>>>>>> > I.e. in the manual it displays -multi='mpi4py' . What it should
>>>>>>>> be is
>>>>>>>> > --multi='mpi4py' . The same goes for -tee. It should be --tee.
>>>>>>>> >
>>>>>>>> > Sincerely,
>>>>>>>> > Sam
>>>>>>>> >
>>>>>>>> _______________________________________________
>>>>>>>> relax (http://www.nmr-relax.com)
>>>>>>>>
>>>>>>>> This is the relax-users mailing list
>>>>>>>> relax-users@gna.org
>>>>>>>>
>>>>>>>> To unsubscribe from this list, get a password
>>>>>>>> reminder, or change your subscription options,
>>>>>>>> visit the list information page at
>>>>>>>> https://mail.gna.org/listinfo/relax-users
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>
>
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